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Conserved domains on  [gi|357431224|gb|AET78289|]
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At1g03560-like protein, partial [Arabidopsis halleri]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 12127860)

pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner

CATH:  1.25.40.10
Gene Ontology:  GO:0003723
PubMed:  19004664|23635770|25882680|34065603|18031283|30809817
SCOP:  4001344

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 4-53 9.25e-17

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 69.70  E-value: 9.25e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 357431224    4 PNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCK 53
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 1-155 1.83e-14

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 69.91  E-value: 1.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYS 80
Cdd:PLN03218  467 GLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFN 546

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 357431224   81 SLIDGLGKVGRVDEAERLFEEM-SE-KGCTRDSYCYNALIDAFTKHGKVDEALALFKrMEEEEGCDQTVYTYTILIS 155
Cdd:PLN03218  547 ALISACGQSGAVDRAFDVLAEMkAEtHPIDPDHITVGALMKACANAGQVDRAKEVYQ-MIHEYNIKGTPEVYTIAVN 622
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 4-53 9.25e-17

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 69.70  E-value: 9.25e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 357431224    4 PNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCK 53
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 1-155 1.83e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 69.91  E-value: 1.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYS 80
Cdd:PLN03218  467 GLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFN 546

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 357431224   81 SLIDGLGKVGRVDEAERLFEEM-SE-KGCTRDSYCYNALIDAFTKHGKVDEALALFKrMEEEEGCDQTVYTYTILIS 155
Cdd:PLN03218  547 ALISACGQSGAVDRAFDVLAEMkAEtHPIDPDHITVGALMKACANAGQVDRAKEVYQ-MIHEYNIKGTPEVYTIAVN 622
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 109-159 1.40e-13

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 61.23  E-value: 1.40e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 357431224  109 RDSYCYNALIDAFTKHGKVDEALALFKRMeEEEGCDQTVYTYTILISGMFK 159
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEM-KKRGVKPNVYTYTILINGLCK 50
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 5-95 3.87e-11

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 60.27  E-value: 3.87e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKT-CRFNGLAINSMFYSSLI 83
Cdd:PLN03081 390 NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSmSENHRIKPRAMHYACMI 469

                         90
                 ....*....|..
gi 357431224  84 DGLGKVGRVDEA 95
Cdd:PLN03081 470 ELLGREGLLDEA 481
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 79-111 6.48e-08

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 46.29  E-value: 6.48e-08
                          10        20        30
                  ....*....|....*....|....*....|...
gi 357431224   79 YSSLIDGLGKVGRVDEAERLFEEMSEKGCTRDS 111
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 8-41 8.78e-08

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 45.91  E-value: 8.78e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 357431224    8 IYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDV 41
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 5-142 1.39e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 46.65  E-value: 1.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEgfKPDVVTYsvvvnglckngRVEEALDYFKTcrfnglainsmfysslid 84
Cdd:COG2956   41 TVEAHLALGNLYRRRGEYDRAIRIHQKLLER--DPDRAEA-----------LLELAQDYLKA------------------ 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 357431224  85 glgkvGRVDEAERLFEEMSEKGcTRDSYCYNALIDAFTKHGKVDEALALFKRMEEEEG 142
Cdd:COG2956   90 -----GLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGP 141
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 4-53 9.25e-17

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 69.70  E-value: 9.25e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 357431224    4 PNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCK 53
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 1-155 1.83e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 69.91  E-value: 1.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYS 80
Cdd:PLN03218  467 GLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFN 546

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 357431224   81 SLIDGLGKVGRVDEAERLFEEM-SE-KGCTRDSYCYNALIDAFTKHGKVDEALALFKrMEEEEGCDQTVYTYTILIS 155
Cdd:PLN03218  547 ALISACGQSGAVDRAFDVLAEMkAEtHPIDPDHITVGALMKACANAGQVDRAKEVYQ-MIHEYNIKGTPEVYTIAVN 622
PLN03077 PLN03077
Protein ECB2; Provisional
 3-128 8.17e-14

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 67.95  E-value: 8.17e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   3 KPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFN-GLAINSMFYSS 81
Cdd:PLN03077 551 EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYAC 630

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 357431224  82 LIDGLGKVGRVDEAERLFEEMSekgCTRDSYCYNALIDAFTKHGKVD 128
Cdd:PLN03077 631 VVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNACRIHRHVE 674
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 109-159 1.40e-13

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 61.23  E-value: 1.40e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 357431224  109 RDSYCYNALIDAFTKHGKVDEALALFKRMeEEEGCDQTVYTYTILISGMFK 159
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEM-KKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 4-140 6.30e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 65.28  E-value: 6.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    4 PNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYSSLI 83
Cdd:PLN03218  435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 357431224   84 DGLGKVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKRMEEE 140
Cdd:PLN03218  515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAE 571
PLN03077 PLN03077
Protein ECB2; Provisional
 5-157 1.95e-12

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 63.72  E-value: 1.95e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMideGFKpDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYSSLID 84
Cdd:PLN03077 322 DVSVCNSLIQMYLSLGSWGEAEKVFSRM---ETK-DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLS 397

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 357431224  85 GLGKVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKRMEEEEgcdqtVYTYTILISGM 157
Cdd:PLN03077 398 ACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKD-----VISWTSIIAGL 465
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 75-123 2.36e-12

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 58.14  E-value: 2.36e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 357431224   75 NSMFYSSLIDGLGKVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTK 123
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 5-155 9.60e-12

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 61.79  E-value: 9.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVN---GLCKNGRVEEAldYFKTCRFnGLAINSMFYSS 81
Cdd:PLN03077 151 DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRtcgGIPDLARGREV--HAHVVRF-GFELDVDVVNA 227

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 357431224  82 LIDGLGKVGRVDEAERLFEEMSekgcTRDSYCYNALIDAFTKHGKVDEALALFKRMEEEEgCDQTVYTYTILIS 155
Cdd:PLN03077 228 LITMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMRELS-VDPDLMTITSVIS 296
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 12-137 1.46e-11

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 61.42  E-value: 1.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224  12 LIDGYAKSGSVEDAirllQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYS----------- 80
Cdd:PLN03081 265 LIDMYSKCGDIEDA----RCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSimirifsrlal 340

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224  81 ------------------------SLIDGLGKVGRVDEAERLFEEMSEkgctRDSYCYNALIDAFTKHGKVDEALALFKR 136
Cdd:PLN03081 341 lehakqahaglirtgfpldivantALVDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAGYGNHGRGTKAVEMFER 416


                 .
gi 357431224 137 M 137
Cdd:PLN03081 417 M 417
PLN03077 PLN03077
Protein ECB2; Provisional
 6-161 2.98e-11

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 60.63  E-value: 2.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   6 VAIYTVLIDGYAKSGSVEDAIRLLQRMIDEgfkpDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNgLAINSMFYSSLIDG 85
Cdd:PLN03077 424 VVVANALIEMYSKCKCIDKALEVFHNIPEK----DVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSA 498

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 357431224  86 LGKVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKrmeeeeGCDQTVYTYTILISGmFKEH 161
Cdd:PLN03077 499 CARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFN------SHEKDVVSWNILLTG-YVAH 567
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 5-95 3.87e-11

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 60.27  E-value: 3.87e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKT-CRFNGLAINSMFYSSLI 83
Cdd:PLN03081 390 NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSmSENHRIKPRAMHYACMI 469

                         90
                 ....*....|..
gi 357431224  84 DGLGKVGRVDEA 95
Cdd:PLN03081 470 ELLGREGLLDEA 481
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 3-157 4.56e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 59.89  E-value: 4.56e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    3 KPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEG--FKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGL-------- 72
Cdd:PLN03218  539 KPDRVVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIkgtpevyt 618

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   73 -AINS--------------------------MFYSSLIDGLGKVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHG 125
Cdd:PLN03218  619 iAVNScsqkgdwdfalsiyddmkkkgvkpdeVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAK 698

                         170       180       190
                  ....*....|....*....|....*....|..
gi 357431224  126 KVDEALALFKRMeEEEGCDQTVYTYTILISGM 157
Cdd:PLN03218  699 NWKKALELYEDI-KSIKLRPTVSTMNALITAL 729
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 5-154 3.04e-10

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 57.57  E-value: 3.04e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEeALDYFKTCRFNGLAINSMFYS-SLI 83
Cdd:PLN03081 188 NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSAR-AGQQLHCCVLKTGVVGDTFVScALI 266

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 357431224  84 DGLGKVGRVDEAERLFEEMSEKgctrDSYCYNALIDAFTKHGKVDEALALFKRMeEEEGCDQTVYTYTILI 154
Cdd:PLN03081 267 DMYSKCGDIEDARCVFDGMPEK----TTVAWNSMLAGYALHGYSEEALCLYYEM-RDSGVSIDQFTFSIMI 332
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 9-154 3.88e-09

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 54.49  E-value: 3.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   9 YTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYF-KTCRFNGLAINSmfyssLIDGLG 87
Cdd:PLN03081 328 FSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFdRMPRKNLISWNA-----LIAGYG 402

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 357431224  88 KVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKRMEEEEGCDQTVYTYTILI 154
Cdd:PLN03081 403 NHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMI 469
PLN03077 PLN03077
Protein ECB2; Provisional
 5-156 4.42e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 54.09  E-value: 4.42e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMIdegfKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYSSLID 84
Cdd:PLN03077 221 DVDVVNALITMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVIS 296

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 357431224  85 GLGKVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKRMEEEEgcdqtVYTYTILISG 156
Cdd:PLN03077 297 ACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKD-----AVSWTAMISG 363
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 105-138 4.77e-09

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 49.27  E-value: 4.77e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 357431224  105 KGCTRDSYCYNALIDAFTKHGKVDEALALFKRME 138
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 35-65 5.36e-09

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 48.88  E-value: 5.36e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 357431224   35 EGFKPDVVTYSVVVNGLCKNGRVEEALDYFK 65
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLD 31
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 1-140 4.39e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 51.42  E-value: 4.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYS 80
Cdd:PLN03218  644 GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMN 723

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   81 SLIDGLGKVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKRMEEE 140
Cdd:PLN03218  724 ALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKED 783
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 79-111 6.48e-08

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 46.29  E-value: 6.48e-08
                          10        20        30
                  ....*....|....*....|....*....|...
gi 357431224   79 YSSLIDGLGKVGRVDEAERLFEEMSEKGCTRDS 111
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 8-41 8.78e-08

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 45.91  E-value: 8.78e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 357431224    8 IYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDV 41
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 79-107 2.25e-07

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 44.76  E-value: 2.25e-07
                          10        20
                  ....*....|....*....|....*....
gi 357431224   79 YSSLIDGLGKVGRVDEAERLFEEMSEKGC 107
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03077 PLN03077
Protein ECB2; Provisional
 19-137 2.94e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 48.69  E-value: 2.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224  19 SGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNgLCKNGRVEEALDY-----FKTCRFNGLAINSMFYSSLIdglgKVGRVD 93
Cdd:PLN03077  64 HGQLEQALKLLESMQELRVPVDEDAYVALFR-LCEWKRAVEEGSRvcsraLSSHPSLGVRLGNAMLSMFV----RFGELV 138

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 357431224  94 EAERLFEEMSEkgctRDSYCYNALIDAFTKHGKVDEALALFKRM 137
Cdd:PLN03077 139 HAWYVFGKMPE----RDLFSWNVLVGGYAKAGYFDEALCLYHRM 178
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 1-32 7.58e-07

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 43.49  E-value: 7.58e-07
                          10        20        30
                  ....*....|....*....|....*....|..
gi 357431224    1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRM 32
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 112-140 7.64e-07

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 43.22  E-value: 7.64e-07
                          10        20
                  ....*....|....*....|....*....
gi 357431224  112 YCYNALIDAFTKHGKVDEALALFKRMEEE 140
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEK 29
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 5-142 1.39e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 46.65  E-value: 1.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEgfKPDVVTYsvvvnglckngRVEEALDYFKTcrfnglainsmfysslid 84
Cdd:COG2956   41 TVEAHLALGNLYRRRGEYDRAIRIHQKLLER--DPDRAEA-----------LLELAQDYLKA------------------ 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 357431224  85 glgkvGRVDEAERLFEEMSEKGcTRDSYCYNALIDAFTKHGKVDEALALFKRMEEEEG 142
Cdd:COG2956   90 -----GLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGP 141
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 112-140 1.79e-06

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 42.44  E-value: 1.79e-06
                          10        20
                  ....*....|....*....|....*....
gi 357431224  112 YCYNALIDAFTKHGKVDEALALFKRMEEE 140
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKER 29
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 97-155 2.52e-06

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 42.73  E-value: 2.52e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 357431224   97 RLFEEMSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKRMeEEEGCDQTVYTYTILIS 155
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERM-KKKGIKPTLDTYNAILG 58
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 16-136 4.34e-06

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 44.03  E-value: 4.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224  16 YAKSGSVEDAIRLLQRMIDEgFKPDVVTYSVVVNGLCKNGRVEEALDYFKtcrfNGLAI---NSMFYSSLIDGLGKVGRV 92
Cdd:COG4783   14 LLLAGDYDEAEALLEKALEL-DPDNPEAFALLGEILLQLGDLDEAIVLLH----EALELdpdEPEARLNLGLALLKAGDY 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 357431224  93 DEAERLFEEMSEKGcTRDSYCYNALIDAFTKHGKVDEALALFKR 136
Cdd:COG4783   89 DEALALLEKALKLD-PEHPEAYLRLARAYRALGRPDEAIAALEK 131
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 8-37 5.36e-06

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 40.91  E-value: 5.36e-06
                          10        20        30
                  ....*....|....*....|....*....|
gi 357431224    8 IYTVLIDGYAKSGSVEDAIRLLQRMIDEGF 37
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
16-136 1.52e-05

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 43.46  E-value: 1.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224  16 YAKSGSVEDAIRLLQRMIDegFKPD-VVTYSVVVNGLCKNGRVEEALDYFKtcrfNGLAINSMFYSSLIdGLGKV----G 90
Cdd:COG0457   18 YRRLGRYEEAIEDYEKALE--LDPDdAEALYNLGLAYLRLGRYEEALADYE----QALELDPDDAEALN-NLGLAlqalG 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 357431224  91 RVDEAERLFEEmSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKR 136
Cdd:COG0457   91 RYEEALEDYDK-ALELDPDDAEALYNLGLALLELGRYDEAIEAYER 135
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 3-83 2.00e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 43.71  E-value: 2.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    3 KPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYSSL 82
Cdd:PLN03218  716 RPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI 795


                  .
gi 357431224   83 I 83
Cdd:PLN03218  796 T 796
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 1-54 2.03e-05

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 40.42  E-value: 2.03e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 357431224    1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKN 54
Cdd:pfam13812  10 GIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 88-140 3.13e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 42.94  E-value: 3.13e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 357431224  88 KVGRVDEAERLFEEMSEkgctRDSYCYNALIDAFTKHGKVDEALALFKRMEEE 140
Cdd:PLN03081 170 KCGMLIDARRLFDEMPE----RNLASWGTIIGGLVDAGNYREAFALFREMWED 218
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 42-65 1.17e-04

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.44  E-value: 1.17e-04
                          10        20
                  ....*....|....*....|....
gi 357431224   42 VTYSVVVNGLCKNGRVEEALDYFK 65
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFK 24
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 54-141 2.33e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 40.10  E-value: 2.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224  54 NGRVEEALDYFKtcrfNGLAINSMFYSSLIdGLGKV----GRVDEAERLFEEMSEKGCTRDSYcYNALIDAFTKHGKVDE 129
Cdd:COG2956   21 NGQPDKAIDLLE----EALELDPETVEAHL-ALGNLyrrrGEYDRAIRIHQKLLERDPDRAEA-LLELAQDYLKAGLLDR 94

                         90
                 ....*....|..
gi 357431224 130 ALALFKRMEEEE 141
Cdd:COG2956   95 AEELLEKLLELD 106
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 51-136 2.53e-04

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 39.17  E-value: 2.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224  51 LCKNGRVEEALDYFKTCrfngLAI---NSMFYSSLIDGLGKVGRVDEAERLFEEMSEKGcTRDSYCYNALIDAFTKHGKV 127
Cdd:COG5010   64 YNKLGDFEESLALLEQA----LQLdpnNPELYYNLALLYSRSGDKDEAKEYYEKALALS-PDNPNAYSNLAALLLSLGQD 138


                 ....*....
gi 357431224 128 DEALALFKR 136
Cdd:COG5010  139 DEAKAALQR 147
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 42-65 2.98e-04

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.66  E-value: 2.98e-04
                          10        20
                  ....*....|....*....|....
gi 357431224   42 VTYSVVVNGLCKNGRVEEALDYFK 65
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFK 24
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 5-137 3.96e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 39.33  E-value: 3.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   5 NVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEgfKPDVVTYSVVVNGLC-KNGRVEEALDYFKtcrfNGLAINSMF---YS 80
Cdd:COG2956  143 NAHAYCELAELYLEQGDYDEAIEALEKALKL--DPDCARALLLLAELYlEQGDYEEAIAALE----RALEQDPDYlpaLP 216

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 357431224  81 SLIDGLGKVGRVDEAERLFEEMSEKgcTRDSYCYNALIDAFTKHGKVDEALALFKRM 137
Cdd:COG2956  217 RLAELYEKLGDPEEALELLRKALEL--DPSDDLLLALADLLERKEGLEAALALLERQ 271
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 1-106 1.53e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 37.93  E-value: 1.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYS 80
Cdd:PLN03218  679 GIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYS 758

                          90       100
                  ....*....|....*....|....*.
gi 357431224   81 SLIDGLGKVGRVDEAERLFEEMSEKG 106
Cdd:PLN03218  759 ILLVASERKDDADVGLDLLSQAKEDG 784
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 27-88 1.70e-03

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 35.03  E-value: 1.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 357431224   27 RLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYSSLIDGLGK 88
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
MRP-S27 pfam10037
Mitochondrial 28S ribosomal protein S27; Members of this family of small ribosomal proteins ...
 28-145 4.51e-03

Mitochondrial 28S ribosomal protein S27; Members of this family of small ribosomal proteins possess one of three conserved blocks of sequence found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins, leaving open the possibility that MRP-S27 might be a functional partner of GTP-binding ribosomal proteins.


Pssm-ID: 462947 [Multi-domain]  Cd Length: 395  Bit Score: 36.26  E-value: 4.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   28 LLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDY---FKTCRFNGLAINSMFYSsLIDGLGKVGRVDEAERLFEEMSE 104
Cdd:pfam10037  55 EMDKTFERKLPVSSLDVDRFVNNISSREEIDDAEYYlykLRHSPNCWYLRDWTSHA-WIRQCLKYGAPDKALYTLKNKVQ 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 357431224  105 KGCTRDSYCYNALIDAFTKHGKVDEALALFKRMEEEEGCDQ 145
Cdd:pfam10037 134 YGIFPDNFTFNLLMDSFLKNGDYKSAASVVTELMLQEAFDN 174
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 13-138 4.90e-03

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 35.84  E-value: 4.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   13 IDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNgLCKNGRV------EEALDY----FKTCRFNGLAINSMFYSSL 82
Cdd:pfam17177  18 LDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLY-LCSKAADatdlkpQLAADRgfevFEAMKAQGVSPNEATYTAV 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 357431224   83 IDGLGKVGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHGKVDEALALFKRME 138
Cdd:pfam17177  97 ARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHML 152
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 1-100 5.29e-03

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 35.84  E-value: 5.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224    1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDEGFKPDVVTYSVVVNGLCKNGRVEEALDYFKTCRFNGLAINSMFYS 80
Cdd:pfam17177  85 GVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELA 164

                          90       100
                  ....*....|....*....|
gi 357431224   81 SLIDGLGKVGRVDEAERLFE 100
Cdd:pfam17177 165 ALLKVSAKAGRADKVYAYLH 184
TPR_16 pfam13432
Tetratricopeptide repeat; This family is found predominantly at the C-terminus of ...
 82-140 5.82e-03

Tetratricopeptide repeat; This family is found predominantly at the C-terminus of transglutaminase enzyme core regions.


Pssm-ID: 433202 [Multi-domain]  Cd Length: 68  Bit Score: 33.85  E-value: 5.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 357431224   82 LIDGLGKVGRVDEAERLFEEMSEKGCT--RDSYCYNALIDAFTKHGKVDEALALFKRMEEE 140
Cdd:pfam13432   3 LARAALRAGDYDDAAAALEAALARFPEspDAAAALLLLGLAALRQGRLAEAAAAYRAALRA 63
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
16-105 6.25e-03

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 34.38  E-value: 6.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224  16 YAKSGSVEDAIRLLQRMIDegFKPD-VVTYSVVVNGLCKNGRVEEALDYFKTCRFNglAINSMFYSSLIDGLGKVGRVDE 94
Cdd:COG3063    2 YLKLGDLEEAEEYYEKALE--LDPDnADALNNLGLLLLEQGRYDEAIALEKALKLD--PNNAEALLNLAELLLELGDYDE 77

                         90
                 ....*....|.
gi 357431224  95 AERLFEEMSEK 105
Cdd:COG3063   78 ALAYLERALEL 88
PLN03077 PLN03077
Protein ECB2; Provisional
 1-113 7.30e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 35.98  E-value: 7.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 357431224   1 GSKPNVAIYTVLIDGYAKSGSVEDAIRLLQRMIDE-GFKPDVVTYSVVVNGLCKNGRVEEALDYFK-------------- 65
Cdd:PLN03077 584 GVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYACVVDLLGRAGKLTEAYNFINkmpitpdpavwgal 663

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 357431224  66 --TCRFN------GLAINSMF---------YSSLIDGLGKVGRVDEAERLFEEMSEKGCTRDSYC 113
Cdd:PLN03077 664 lnACRIHrhvelgELAAQHIFeldpnsvgyYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGC 728
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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